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A genome-wide scan of copy number variants using high-density SNPs in Brown Swiss dairy cattle

Research paper by R.T.M.M. Prinsen, M.G. Strillacci, F. Schiavini, E. Santus, A. Rossoni, V. Maurer, A. Bieber, B. Gredler, M. Dolezal, A. Bagnato

Indexed on: 05 Oct '16Published on: 05 Aug '16Published in: Livestock Science



Abstract

Detecting genetic variation such as Copy Number Variants (CNVs) in cattle provides the opportunity to study their association with quantitative traits. CNVs are DNA sequences of 50 bp up to several Mb long, which can vary in copy number in comparison with a reference genome. The aim of this study was to investigate CNVs in 1410 samples of the Brown Swiss cattle breed using Illumina Bovine HD SNP chip information, which includes 777,962 SNPs. After stringent quality control, CNVs were called with the Golden Helix SVS 8.3.1 (SVS) and PennCNV software and were summarized to CNV regions (CNVRs) at a population level (i.e. overlapping CNVs), using BEDTools. Additionally, common CNVRs between the two software were set as consensus regions. Genes within consensus CNVRs were annotated with a GO analysis using the DAVID Bioinformatics Resources 6.7. In order to validate these results, quantitative PCRs were executed on 15 selected CNVRs.

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